Browsing by Author "Duru, Ilhan Cem"

Lactobacilli are gram-positive lactic acid bacteria with wide beneficial properties for human health and food production. Today most of the fermented products and probiotic foods are produced by lactobacilli species. One of the most using area of lactobacilli species is fermented products especially dairy products. Lactobacilli species can be used as starter or adjunct cultures in dairy products and play important role for preservation and quality, texture and flavor formation. Additionally, probiotic properties of lactobacilli species provide several health effect for human by stimulation of immune system and protection against pathogens. Lactobacillus rhamnosus LC705 is a facultatively heterofermentative type lactobacilli which is used in production of dairy products as adjunct starter and protective culture. The complete and annotated genome sequence of L. rhamnosus strain LC705 published on 2009. Known characteristics of L. rhamnosus strain LC705 are food preservation, toxin removal and health benefits when combined with other probiotic strains. However, molecular mechanism behind these characteristics are not known or not clearly understood. To get further insight on these properties and roles in cheese ripening of strain LC705, we re-annotated genome of the LC705 with updated methods and databases, analyzed metabolic pathways of LC705, and performed RNA-seq experiment to determine gene expression changes of LC705 during warm room (25 °C) and cold room (5 °C) cheese ripening process. Several un-characterized proteins of LC705 were annotated (77) and 1197 enzyme commission (EC) numbers are added to annotation file with re-annotation of genes of LC705. More importantly, re-annotation provided us 72 new pathways of LC705 which is 35% of the entire collection of 201 pathways. Analyzes of pathways showed that genome of LC705 has responsible genes for production of flavor compounds such as acetoin and diacetyl which are provide buttery flavor to dairy products, and hydrogen sulfide which is a volatile sulfur compound that cause unlikeable odor. Additionally to flavor compounds, we defined genes that produce anti-fungus compounds and bacteriocin which provide food preservation characteristic to LC705. Determination of gene expression respond of LC705 during warm room and cold room cheese ripening process with RNA-Seq showed that central metabolism genes that responsible for lyase activity, degradation activity, disaccharides and monosaccharides metabolism are warm induced genes. The genes play role in citrate metabolism pathways were significantly down-regulated during cold room, citrate degradation pathways are critical for buttery flavor products, therefore buttery flavor compounds are produced by LC705 during warm room. Finally, during cold room ripening, the genes of LC705 that produces ethanol and acetyl-CoA from pyruvate was up-regulated, so we may say that LC705 uses pyruvate to produce ethanol and acetyl-CoA instead of lactic acid.